I very much agree and the only thing that I'm missing is tools that generate a somewhat stable output. What I want is tools that take their last output into consideration and generate new diagrams that are both correct and as similar as possible to the last output they produced. They should do what a human does out of necessity when updating a diagram manually - make it represent the current state correctly with minimal effort.

Of course that means the diagrams will not be optimal in any case. For example, there could be better arrangements of boxes or less crossings of lines. I sill think stable diagrams are important for our limited brain and one important reason why people shy away from automatic diagram generation is the mental chaos a complete rearrangement of elements brings with it.

One example of a software that got this right is Taskjuggler, the obvious counterexample is Graphviz.